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fix sambamba depth stub version #9509

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Merged
fellen31 merged 2 commits into from
Dec 5, 2025
Merged

fix sambamba depth stub version #9509

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70538f3
fix stub version
fellen31 Dec 5, 2025
582c1a8
stray module
fellen31 Dec 5, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/sambamba/depth/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ process SAMBAMBA_DEPTH {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sambamba: \$(sambamba --version)
sambamba: \$(echo \$(sambamba --version 2>&1) | awk '{print \$2}' )
END_VERSIONS
"""
}
10 changes: 8 additions & 2 deletions modules/nf-core/sambamba/depth/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,10 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out,
process.out.versions.collect{ path(it).yaml }
).match() }
)
}
}
Expand Down Expand Up @@ -85,7 +88,10 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out,
process.out.versions.collect{ path(it).yaml }
).match() }
)
}
}
Expand Down
40 changes: 27 additions & 13 deletions modules/nf-core/sambamba/depth/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,10 @@
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-12-03T15:57:58.097957"
"timestamp": "2025-12-05T12:03:11.190921915"
},
"test-sambamba-depth": {
"content": [
Expand Down Expand Up @@ -61,13 +61,20 @@
"versions": [
"versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57"
]
}
},
[
{
"SAMBAMBA_DEPTH": {
"sambamba": "1.0.1"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-12-03T15:57:42.031913"
"timestamp": "2025-12-05T12:03:07.689091449"
},
"test-sambamba-depth-stub": {
"content": [
Expand All @@ -82,7 +89,7 @@
]
],
"1": [
"versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce"
"versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57"
],
"bed": [
[
Expand All @@ -94,14 +101,21 @@
]
],
"versions": [
"versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce"
"versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57"
]
}
},
[
{
"SAMBAMBA_DEPTH": {
"sambamba": "1.0.1"
}
}
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-12-03T15:58:13.647811"
"timestamp": "2025-12-05T12:03:14.737096819"
}
}
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